Pirat

Installation

To install this package from Github:

install.packages('BiocManager')
BiocManager::install('edyp-lab/Pirat', version = 'devel')

Test

library(Pirat)
data(subbouyssie)
my_pipeline_llkimpute(subbouyssie) 

data(subropers)
nsamples = nrow(subropers$peptides_ab)
my_pipeline_llkimpute(subropers, 
extension = "T",
rna.cond.mask = 1:nsamples, 
pep.cond.mask = 1:nsamples,
max.pg.size.pirat.t = 1)

Note: If you run the imputation function my_pipeline_llkimpute() for the first time after the installation of the package, Pirat will automatically install the Python environment needed to process imputation computations. This function takes a long time to execute but need to be run only once.